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- PDB-6ox5: A SETD3 Mutant (N255A) in Complex with an Actin Peptide with His7... -

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Basic information

Entry
Database: PDB / ID: 6ox5
TitleA SETD3 Mutant (N255A) in Complex with an Actin Peptide with His73 Replaced with Lysine
Components
  • Actin Peptide
  • Actin-histidine N-methyltransferase
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / TRANSFERASE / TRANSFERASE-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport ...peptidyl-histidine methylation / regulation of uterine smooth muscle contraction / protein-histidine N-methyltransferase / protein-L-histidine N-tele-methyltransferase activity / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / histone H3K36 methyltransferase activity / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Formation of annular gap junctions / Tat protein binding / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / apical protein localization / regulation of double-strand break repair / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / histone H3K4 methyltransferase activity / tight junction / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nitric-oxide synthase binding / positive regulation of muscle cell differentiation / positive regulation of double-strand break repair / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / regulation of synaptic vesicle endocytosis / regulation of G1/S transition of mitotic cell cycle / brush border / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / calyx of Held / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / adherens junction / positive regulation of cell differentiation / actin filament / FCGR3A-mediated phagocytosis / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / Schaffer collateral - CA1 synapse / B-WICH complex positively regulates rRNA expression / kinetochore / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / PKMTs methylate histone lysines / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / tau protein binding / VEGFA-VEGFR2 Pathway / platelet aggregation / cytoplasmic ribonucleoprotein granule / nuclear matrix / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / UCH proteinases / Signaling by BRAF and RAF1 fusions
Similarity search - Function
Actin-histidine N-methyltransferase SETD3 / SETD3, SET domain / SETD3 actin-histidine N-methyltransferase (EC 2.1.1.85) family profile. / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / SET domain / SET domain superfamily / SET domain profile. ...Actin-histidine N-methyltransferase SETD3 / SETD3, SET domain / SETD3 actin-histidine N-methyltransferase (EC 2.1.1.85) family profile. / Rubisco LSMT, substrate-binding domain / Rubisco LSMT, substrate-binding domain superfamily / : / Rubisco LSMT substrate-binding / SET domain / SET domain superfamily / SET domain profile. / SET domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Actin, cytoplasmic 1 / Actin-histidine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 Å
AuthorsHorton, J.R. / Dai, S. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
Citation
Journal: Nat Commun / Year: 2019
Title: Structural basis for the target specificity of actin histidine methyltransferase SETD3.
Authors: Dai, S. / Horton, J.R. / Woodcock, C.B. / Wilkinson, A.W. / Zhang, X. / Gozani, O. / Cheng, X.
#1: Journal: Nature / Year: 2019
Title: SETD3 is an actin histidine methyltransferase that prevents primary dystocia.
Authors: Wilkinson, A.W. / Diep, J. / Dai, S. / Liu, S. / Ooi, Y.S. / Song, D. / Li, T.M. / Horton, J.R. / Zhang, X. / Liu, C. / Trivedi, D.V. / Ruppel, K.M. / Vilches-Moure, J.G. / Casey, K.M. / ...Authors: Wilkinson, A.W. / Diep, J. / Dai, S. / Liu, S. / Ooi, Y.S. / Song, D. / Li, T.M. / Horton, J.R. / Zhang, X. / Liu, C. / Trivedi, D.V. / Ruppel, K.M. / Vilches-Moure, J.G. / Casey, K.M. / Mak, J. / Cowan, T. / Elias, J.E. / Nagamine, C.M. / Spudich, J.A. / Cheng, X. / Carette, J.E. / Gozani, O.
History
DepositionMay 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: Actin Peptide
A: Actin-histidine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,74611
Polymers69,8652
Non-polymers8819
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint11 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.465, 116.497, 174.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

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Components

#1: Protein/peptide Actin Peptide


Mass: 2154.438 Da / Num. of mol.: 1 / Mutation: H73K / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P60709
#2: Protein Actin-histidine N-methyltransferase / SET domain-containing protein 3 / hSETD3


Mass: 67710.484 Da / Num. of mol.: 1 / Mutation: N255A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD3, C14orf154 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86TU7, protein-histidine N-methyltransferase
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H20N6O5S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→34.94 Å / Num. obs: 35098 / % possible obs: 96.6 % / Redundancy: 16.1 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.036 / Net I/σ(I): 18.5
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2968 / CC1/2: 0.384 / Rpim(I) all: 0.45 / % possible all: 82.9

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MBJ

6mbj


Resolution: 2.098→34.938 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 1750 5 %
Rwork0.1627 --
obs0.1649 35025 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.098→34.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 58 235 4264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044154
X-RAY DIFFRACTIONf_angle_d0.6325635
X-RAY DIFFRACTIONf_dihedral_angle_d16.0012482
X-RAY DIFFRACTIONf_chiral_restr0.043624
X-RAY DIFFRACTIONf_plane_restr0.004720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0982-2.15490.2471040.21051987X-RAY DIFFRACTION75
2.1549-2.21830.21291180.2072254X-RAY DIFFRACTION86
2.2183-2.28990.26551260.20542373X-RAY DIFFRACTION90
2.2899-2.37170.22341350.18582570X-RAY DIFFRACTION98
2.3717-2.46670.2321380.18672636X-RAY DIFFRACTION99
2.4667-2.57890.22861380.1782618X-RAY DIFFRACTION99
2.5789-2.71480.21581390.17352656X-RAY DIFFRACTION100
2.7148-2.88480.20711400.17122651X-RAY DIFFRACTION100
2.8848-3.10740.22381400.16832665X-RAY DIFFRACTION100
3.1074-3.41990.19411400.16532654X-RAY DIFFRACTION99
3.4199-3.91420.17811400.14252684X-RAY DIFFRACTION100
3.9142-4.92930.19451440.13662715X-RAY DIFFRACTION100
4.9293-34.94230.19521480.15972812X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9339-0.0789-0.65121.1005-0.05941.38580.1544-0.39380.27240.1503-0.0004-0.0816-0.25670.2302-0.12450.2306-0.04620.01790.2714-0.05710.2295-22.3709-3.314-28.3973
21.4819-0.85781.5731.0078-1.66813.3820.0815-0.1821-0.227-0.0494-0.00160.01340.3355-0.0891-0.04410.26450.0039-0.01140.23820.06080.2416-28.8006-33.3009-8.3987
35.13015.47080.47286.09120.06034.8980.1576-0.64820.01351.97350.0829-2.17980.59041.5179-0.25450.4951-0.0082-0.19320.979-0.04680.51-3.5622-14.385-19.7964
48.3303-5.5067-3.57786.50744.85363.6968-0.6701-1.2497-0.39630.62860.04230.02350.74990.6840.5620.3104-0.00030.03330.5666-0.02060.2218-15.3591-11.6995-24.0265
55.4001-4.5384-3.5396.3442.26572.5335-0.4816-0.918-0.1761.1950.06320.6317-0.19670.00780.44870.5398-0.00960.04790.7138-0.08920.3853-26.5119-3.5901-14.3786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 334 )
2X-RAY DIFFRACTION2chain 'A' and (resid 335 through 502 )
3X-RAY DIFFRACTION3chain 'Y' and (resid 66 through 70 )
4X-RAY DIFFRACTION4chain 'Y' and (resid 71 through 75 )
5X-RAY DIFFRACTION5chain 'Y' and (resid 76 through 83 )

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